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{{Coexpression_clusters
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U6!0.00312021664900506!25804$GO:0006396!RNA processing!0.00445686189516397!10248;25804$GO:0030681!multimeric ribonuclease P complex!0.00445686189516397!10248$GO:0005655!nucleolar ribonuclease P complex!0.00445686189516397!10248$GO:0030677!ribonuclease P complex!0.00445686189516397!10248$GO:0005684!U2-dependent spliceosome!0.00445686189516397!25804$GO:0004526!ribonuclease P activity!0.00445686189516397!10248$GO:0004549!tRNA-specific ribonuclease activity!0.00584920069324615!10248$GO:0044428!nuclear part!0.0059422257858873!10248;25804$GO:0030529!ribonucleoprotein complex!0.0059422257858873!10248;25804$GO:0030532!small nuclear ribonucleoprotein complex!0.00708889649082795!25804$GO:0016891!endoribonuclease activity, producing 5'-phosphomonoesters!0.00983488969882731!10248$GO:0044452!nucleolar part!0.00983488969882731!10248$GO:0016893!endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.0122482513790345!10248$GO:0004521!endoribonuclease activity!0.0149613887740454!10248$GO:0008033!tRNA processing!0.0179172156272548!10248$GO:0004540!ribonuclease activity!0.0183274711924229!10248$GO:0005681!spliceosome!0.0240460659124371!25804$GO:0004519!endonuclease activity!0.0247427641746072!10248$GO:0005730!nucleolus!0.0256796512216183!10248$GO:0006399!tRNA metabolic process!0.0293575749978811!10248$GO:0032991!macromolecular complex!0.0293575749978811!10248;25804$GO:0008380!RNA splicing!0.0293575749978811!25804$GO:0004518!nuclease activity!0.0293575749978811!10248$GO:0044446!intracellular organelle part!0.0293575749978811!10248;25804$GO:0044422!organelle part!0.0293575749978811!10248;25804$GO:0016070!RNA metabolic process!0.0293575749978811!10248;25804$GO:0006397!mRNA processing!0.0303003199967942!25804$GO:0016071!mRNA metabolic process!0.0366123538767712!25804$GO:0010467!gene 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7069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;1.23283,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;3.85295,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;3.88672,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3766_Alveolar_Renal_chronic_Placental_nonsmall_acute_carcinoid
|gostat_on_coexpression_clusters=GO:0005688!snRNP U6!0.00312021664900506!25804$GO:0006396!RNA processing!0.00445686189516397!10248;25804$GO:0030681!multimeric ribonuclease P complex!0.00445686189516397!10248$GO:0005655!nucleolar ribonuclease P complex!0.00445686189516397!10248$GO:0030677!ribonuclease P complex!0.00445686189516397!10248$GO:0005684!U2-dependent spliceosome!0.00445686189516397!25804$GO:0004526!ribonuclease P activity!0.00445686189516397!10248$GO:0004549!tRNA-specific ribonuclease activity!0.00584920069324615!10248$GO:0044428!nuclear part!0.0059422257858873!10248;25804$GO:0030529!ribonucleoprotein complex!0.0059422257858873!10248;25804$GO:0030532!small nuclear ribonucleoprotein complex!0.00708889649082795!25804$GO:0016891!endoribonuclease activity, producing 5'-phosphomonoesters!0.00983488969882731!10248$GO:0044452!nucleolar part!0.00983488969882731!10248$GO:0016893!endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.0122482513790345!10248$GO:0004521!endoribonuclease activity!0.0149613887740454!10248$GO:0008033!tRNA processing!0.0179172156272548!10248$GO:0004540!ribonuclease activity!0.0183274711924229!10248$GO:0005681!spliceosome!0.0240460659124371!25804$GO:0004519!endonuclease activity!0.0247427641746072!10248$GO:0005730!nucleolus!0.0256796512216183!10248$GO:0006399!tRNA metabolic process!0.0293575749978811!10248$GO:0032991!macromolecular complex!0.0293575749978811!10248;25804$GO:0008380!RNA splicing!0.0293575749978811!25804$GO:0004518!nuclease activity!0.0293575749978811!10248$GO:0044446!intracellular organelle part!0.0293575749978811!10248;25804$GO:0044422!organelle part!0.0293575749978811!10248;25804$GO:0016070!RNA metabolic process!0.0293575749978811!10248;25804$GO:0006397!mRNA processing!0.0303003199967942!25804$GO:0016071!mRNA metabolic process!0.0366123538767712!25804$GO:0010467!gene expression!0.0455277092838167!10248;25804
|id=C3766
|ontology_enrichment_celltype=CL:0000066!1.49e-27!254;CL:0002321!3.07e-21!248;CL:0000220!1.82e-20!246;CL:0000548!1.16e-18!679;CL:0000004!1.16e-18!679;CL:0000255!1.16e-18!679;CL:0000012!4.51e-18!682;CL:0000222!3.38e-09!119;CL:0000003!2.20e-08!722;CL:0000144!3.43e-08!625;CL:0000221!1.08e-07!71;CL:0000076!1.13e-07!62;CL:1000449!2.58e-07!16;CL:1000497!9.47e-07!18;CL:0002518!9.47e-07!18
|ontology_enrichment_disease=DOID:162!1.76e-24!235;DOID:14566!1.89e-24!239;DOID:0050687!7.92e-14!143;DOID:0050686!2.21e-11!137;DOID:2531!7.77e-11!51;DOID:0060083!7.77e-11!51;DOID:305!5.47e-10!106;DOID:1240!6.53e-09!39;DOID:8692!4.67e-07!31
|ontology_enrichment_uberon=UBERON:0003104!1.52e-09!238;UBERON:0009142!1.52e-09!238;UBERON:0000072!1.61e-07!46;UBERON:0002100!2.38e-07!216;UBERON:0004211!2.58e-07!16;UBERON:0001285!2.58e-07!16;UBERON:0007684!2.58e-07!16;UBERON:0003220!2.58e-07!16;UBERON:0004208!2.58e-07!16;UBERON:0005256!4.18e-07!143;UBERON:0000119!4.81e-07!312;UBERON:0008947!7.16e-07!38;UBERON:0003258!7.16e-07!38
}}

Latest revision as of 12:32, 17 September 2013


Full id: C3766_Alveolar_Renal_chronic_Placental_nonsmall_acute_carcinoid



Phase1 CAGE Peaks

Hg19::chr19:18433875..18433909,-p1@LSM4
Hg19::chr19:18433910..18433944,-p2@LSM4
Hg19::chr7:100303728..100303787,+p1@POP7


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0005688snRNP U60.00312021664900506
GO:0006396RNA processing0.00445686189516397
GO:0030681multimeric ribonuclease P complex0.00445686189516397
GO:0005655nucleolar ribonuclease P complex0.00445686189516397
GO:0030677ribonuclease P complex0.00445686189516397
GO:0005684U2-dependent spliceosome0.00445686189516397
GO:0004526ribonuclease P activity0.00445686189516397
GO:0004549tRNA-specific ribonuclease activity0.00584920069324615
GO:0044428nuclear part0.0059422257858873
GO:0030529ribonucleoprotein complex0.0059422257858873
GO:0030532small nuclear ribonucleoprotein complex0.00708889649082795
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.00983488969882731
GO:0044452nucleolar part0.00983488969882731
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0122482513790345
GO:0004521endoribonuclease activity0.0149613887740454
GO:0008033tRNA processing0.0179172156272548
GO:0004540ribonuclease activity0.0183274711924229
GO:0005681spliceosome0.0240460659124371
GO:0004519endonuclease activity0.0247427641746072
GO:0005730nucleolus0.0256796512216183
GO:0006399tRNA metabolic process0.0293575749978811
GO:0032991macromolecular complex0.0293575749978811
GO:0008380RNA splicing0.0293575749978811
GO:0004518nuclease activity0.0293575749978811
GO:0044446intracellular organelle part0.0293575749978811
GO:0044422organelle part0.0293575749978811
GO:0016070RNA metabolic process0.0293575749978811
GO:0006397mRNA processing0.0303003199967942
GO:0016071mRNA metabolic process0.0366123538767712
GO:0010467gene expression0.0455277092838167



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell6.16e-30253
embryonic cell2.29e-22250
animal cell3.37e-19679
eukaryotic cell3.37e-19679
mesodermal cell2.69e-10121
squamous epithelial cell8.12e-0963
native cell1.04e-08722
epithelial cell of nephron2.35e-0815
kidney cortical cell1.43e-0712
renal cortical epithelial cell1.43e-0712
kidney cell1.56e-0717
kidney epithelial cell1.56e-0717
non-terminally differentiated cell2.09e-07106
ectodermal cell2.91e-0772
Uber Anatomy
Ontology termp-valuen
trunk1.80e-08199
nephron epithelium2.35e-0815
renal tubule2.35e-0815
nephron tubule2.35e-0815
nephron2.35e-0815
uriniferous tubule2.35e-0815
nephrogenic mesenchyme2.35e-0815
cortex5.47e-0815
epithelial vesicle7.34e-0878
organism subdivision7.94e-08264
unilaminar epithelium8.27e-08148
parenchyma1.11e-0715
cortex of kidney1.43e-0712
renal parenchyma1.43e-0712
excretory tube2.72e-0716
kidney epithelium2.72e-0716
cell layer2.74e-07309
segment of respiratory tract4.27e-0747
larynx6.53e-079
epithelium7.75e-07306
mesenchyme8.98e-07160
entire embryonic mesenchyme8.98e-07160
respiratory primordium9.06e-0738
endoderm of foregut9.06e-0738
Disease
Ontology termp-valuen
disease of cellular proliferation7.77e-22239
cancer7.87e-22235
cell type cancer1.58e-13143
carcinoma4.52e-10106
organ system cancer8.10e-10137
hematologic cancer1.41e-0851
immune system cancer1.41e-0851
leukemia4.71e-0739


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.11.0927
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.13.85295
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.15877
MA0138.23.88672
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467214.97544968400580.005768294540793880.0259558342760005
CCNT2#90536.336201576962630.003930750035764890.018997806607675
CHD2#1106310.34402283411690.0009033701102746880.00660231427200687
E2F1#186934.907389214879320.008460985347239390.0325292416226886
E2F4#1874312.66806031528440.0004917987006298980.004369828526041
E2F6#187635.017155731697390.00791769806886330.0322120863470069
EBF1#187938.9064668465690.00141523283560980.00914921090177978
ELF1#199734.258097958807540.01295179875054610.0462167865828988
ELK4#2005210.8237877723120.01091284719516480.0401934986675065
ETS1#211339.728760922202340.001085840092584840.00761970391920095
GABPB1#255337.067683836182170.002832212825417420.0154059101705089
HMGN3#932438.178547723350590.001827766942164210.0108676431353651
IRF1#365937.63716375356390.002244692747297240.0128028761856249
IRF3#3661231.32130147432640.001339514673320110.008876749553736
MAX#414936.452555509007120.003721913834265510.0186442015893738
MYC#460935.22228187160940.007020843755740150.0294418751658601
NFYA#4800212.28372046655370.008516011403724430.0324730262146692
NFYB#4801211.17319550235760.01025467135054530.0381270068059665
NRF1#4899312.21027944771090.0005492172401020010.00471126893954931
PAX5#507936.669565531177830.003370290999677260.0172866035613051
PBX3#5090214.60967512449610.006056122473217890.0268324866358562
SIN3A#2594235.408884726815140.006318961977991520.0276648949913836
SMARCB1#6598212.16847718743830.008675002221921740.032986549080874
SMC3#9126210.02995522995520.0126656379767470.045745834992858
SP1#666735.69838137814090.005403962701712170.0246402296705574
SP2#6668217.43568699589640.004273568481769740.0203180779654732
THAP1#55145220.91276306856750.002983447413736940.015867406652914
YY1#752834.911170749853860.008441455341808260.0329293375581038



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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